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J Proteome Res. 2016 Jun 3;15(6):1963-70. doi: 10.1021/acs.jproteome.6b00140. Epub 2016 May 2.

A Pipeline for Differential Proteomics in Unsequenced Species.

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Medical Biotechnology Center, VIB , Albert Baertsoenkaai 3, Ghent B-9000, Belgium.
Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
Bioinformatics Institute Ghent, Ghent University , B-9052 Ghent, Belgium.
Veterinary Helminthology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine , 2000 Antwerp, Belgium.
Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Jonas Liesvei 91, N-5009 Bergen, Norway.
Department of Applied Mathematics, Computer Science, and Statistics, Ghent University , B-9000 Ghent, Belgium.
Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands.


Shotgun proteomics experiments often take the form of a differential analysis, where two or more samples are compared against each other. The objective is to identify proteins that are either unique to a specific sample or a set of samples (qualitative differential proteomics), or that are significantly differentially expressed in one or more samples (quantitative differential proteomics). However, the success depends on the availability of a reliable protein sequence database for each sample. To perform such an analysis in the absence of a database, we here propose a novel, generic pipeline comprising an adapted spectral similarity score derived from database search algorithms that compares samples at the spectrum level to detect unique spectra. We applied our pipeline to compare two parasitic tapeworms: Taenia solium and Taenia hydatigena, of which only the former poses a threat to humans. Furthermore, because the genome of T. solium recently became available, we were able to prove the effectiveness and reliability of our pipeline a posteriori.


differential proteomics; mass spectrometry; unique spectrum; unsequenced species

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